mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-14 13:43:09 +00:00
80 lines
2.3 KiB
Markdown
80 lines
2.3 KiB
Markdown
# nf-core/configs: ABiMS Configuration
|
|
|
|
All nf-core pipelines have been successfully configured for use on the ABiMS cluster.
|
|
|
|
To use, run the pipeline with `-profile abims`. This will download and launch the [`abims.config`](../conf/abims.config) which has been pre-configured with a setup suitable for the ABiMS cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
|
|
|
|
## Request an account
|
|
|
|
You will need an account to use the HPC cluster on ABiMS in order
|
|
to run the pipeline. If in doubt see [http://abims.sb-roscoff.fr/account](http://abims.sb-roscoff.fr/account).
|
|
|
|
## Running the workflow on the ABiMS cluster
|
|
|
|
Nextflow is installed on the ABiMS cluster.
|
|
|
|
You need to activate it like this:
|
|
|
|
```bash
|
|
module load nextflow slurm-drmaa graphviz
|
|
```
|
|
|
|
Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command.
|
|
Nextflow shouldn't run directly on the submission node but on a compute node. Run nextflow from a compute node:
|
|
|
|
```bash
|
|
# Load the dependencies if not done before
|
|
module load nextflow slurm-drmaa graphviz
|
|
|
|
# Run a downloaded/git-cloned nextflow workflow from
|
|
srun nextflow run \
|
|
/path/to/nf-core/workflow \
|
|
-profile abims \
|
|
--email my-email@example.org \
|
|
-c my-specific.config
|
|
...
|
|
|
|
# Or use let nf-core client download the workflow
|
|
srun nextflow run nf-core/rnaseq -profile abims ...
|
|
|
|
# To launch in background
|
|
sbatch --wrap "nextflow run nf-core/rnaseq -profile abims ..."
|
|
```
|
|
|
|
Or write a sbatch script
|
|
|
|
> nfcore-rnaseq.sh
|
|
|
|
```bash
|
|
#!/bin/bash
|
|
#SBATCH -p fast
|
|
#SBATCH --mem=4G
|
|
|
|
module load nextflow slurm-drmaa graphviz
|
|
nextflow run nf-core/rnaseq -profile abims ...
|
|
```
|
|
|
|
Launch on the cluster with sbatch:
|
|
|
|
```bash
|
|
sbatch nfcore-rnaseq.sh
|
|
```
|
|
|
|
### Hello, world
|
|
|
|
nf-core provides some test for each workflow:
|
|
|
|
```bash
|
|
module load nextflow slurm-drmaa graphviz
|
|
nextflow run nf-core/rnaseq -profile abims,test
|
|
```
|
|
|
|
## Singularity images mutualized directory
|
|
|
|
To reduce the disk usage, nf-core images can be stored in a mutualized directory: `/shared/software/singularity/images/nf-core/`
|
|
|
|
The environment variable `NXF_SINGULARITY_CACHEDIR: /shared/data/cache/nextflow` will indicate this directory to nextflow.
|
|
|
|
## Databanks
|
|
|
|
A local copy of several genomes are available in `/shared/bank/` directory.
|